Comparative analysis of microsatellite instability-high (MSI-H) <i>BRAF</i> V600E-mutated versus MSI-H <i>BRAF</i>wild type colorectal cancers (CRC), including tumor microenvironment (TME), associated genomic alterations, and immunometabolomic biomarkers.
Authors: Mohamed E. Salem, Scott Kopetz, Sherif Mohamed El-Refai, Josep Tabernero, Frank A. Sinicrope, Jeanne Tie, Thomas J. George, Eric VanCutsem, Elizabeth Mauer, Sara Lonardi, Thierry Andre, Michael J. Overman, David Foureau
Journal: Journal of Clinical Oncology (2022)

3066 Background: The BRAF V600E mutation is associated with the hypermethylator phenotype CIMP, which can also lead to the MSI-H phenotype. BRAF V600E mutation and MSI-H/dMMR status seem to be biologically intertwined; however, the impact of coexisting BRAF V600E mutations on the TME and immunometabolomic features of MSI-H/dMMR CRC tumors is not well characterized. Methods: A retrospective review of deidentified records of patients with MSI-H/dMMR CRC tumors was conducted using next-generation sequencing data (Tempus |xT assay: DNA-seq of 595-648 genes at 500x coverage, and full transcriptome RNA-seq). Several immune markers of tumor immunogenicity in BRAF wild-type ( BRAF wt ) vs. V600E-mutated (BRAF V600E ) tumors were assessed, including tumor mutational burden (TMB), neoantigen tumor burden (NTB, ScanNeo), PD-L1 expression, immune infiltration, and canonical immuno-metabolomic pathways (82 geneset signatures). Results: A total of 459 MSI-H/dMMR CRC tumors were analyzed, of which 123 (27%) tumors harbored BRAF V600E mutations, and 336 (73%) were BRAF wt . MSI-H/dMMR BRAF V600E tumors were more frequently identified in females (69% vs. 55%; P= 0.01), non-Hispanic or non-Latino (100% vs. 73%; P =0.001), and older patients (median age: 76 yrs vs. 62 yrs; P&lt; 0.001). Compared to BRAF WT , BRAF V600E tumors exhibited significantly higher TMB (Median: 49 mut/MB vs. 36 mut/MB; P &lt; 0.001) and were more frequently associated with TMB-High status (&gt; 10 mut/MB; 100% vs. 95%; P = 0.008); however, no significant differences were observed with tumor NTB, immune score, or T cell infiltration (CD4 or CD8). NK cell infiltration was higher in the BRAF V600E cohort (&lt; 0.001). When compared to BRAF WT tumors , BRAF V600E tumors harbored a greater frequency of mutations in MSH6(42% vs. 20%), B2M (33% vs. 16%), BRCA2 (31% vs. 12%), ATM (23% vs. 12%), and TP53 (30% vs. 19%) but a lower frequency of MSH2 (3.3% vs. 11%), all P&lt; 0.05. Pathway enrichment analysis identified 10 significantly altered signaling pathways, most of which related to stromal/immune cell signaling and metabolism. Five were upregulated among BRAF V600E tumors: glycerophospholipid, galactose, cyclin-dependent cell signaling; Nucleotide, and TH1 inflammation. Five pathways were downregulated (Wnt, Notch, TH17 inflammation, amino sugar, and cancer stem cell signaling). Conclusions: MSI-H/dMMR BRAF V600E CRCs undergo broad metabolic reprogramming (e.g., glycerophospholipidgalactose, nucleotide). A rise in lipid metabolism, particularly with NK inflammation, suggests that BRAF V600E mutated tumors may be associated with a non-classical immune component. BRAF V600E and BRAF wt CRCs exhibited similar NTB and T cell infiltration, suggesting that both are likely to benefit from immune checkpoint inhibitors.